generating xsc and vel files

From: David A. Horita (
Date: Mon Feb 02 2009 - 10:29:29 CST

I've run an MD simulation but decided that I'd like to start another run
from the middle of the previous run. I have the dcd and can pick an
intermediate time point and generate starting coordinates for the second
run; is there a way to regenerate the .xsc and .vel files for that
particular time point? (I have the final .coor, .xsc, and .vel, but not
the intermediate ones). I assume that I can always assign velocities
based on a Gaussian distribution if necessary, but how about the .xsc?
(The system is a water/protein/membrane with PME run NPTA. I could
measure the approximate xyz dimensions, but if I had to do that, along
with reassigning velocities, I suspect I'd need to reequilibrate, which
is what I'm trying to avoid...)
David Horita
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016
Tel: 336 713-4194
Fax: 336 716-7671

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